I'm running Windows 7 and Ubuntu on the same machine. When I boot into Windows, the clock is 2 hours behind the actual time. If I fix the time and then boot into Ubuntu, the clock is 2 hours ahead. This upsets the Windows time, and it goes on like a vicious cycle.
Ubuntu gives you the choice to set UTC or not during installation, and if you selected UTC time, your Windows / Ubuntu clocks will keep messing each other up.
You can check this file:
sudo gedit /etc/default/rcS
to see whether UTC=yes. If so change it to UTC=no
Simply changing the clock preferences to display UTC is not the same effect as editing this file.
P.S. Ubuntu is right when it assumes that BIOS time should be UTC time. However Windows is not that "mature" yet. There is a hack to enable Windows but there is apparently a side effect with BIOS time not being updated properly; it could cause more issues than it fixes.
Here is the the reg file to enable the hack
Windows Registry Editor Version 5.00 HKEY_LOCAL_MACHINE\SYSTEM\CurrentCo... “RealTimeIsUniversal”=dword:00000001